Patient25 supragingival 16S_full-length
BioSample: SAMN47767906 · Study: PRJNA1243403 · Body site: Plaque
Interactive report · NCBI SRA · ENA
Relative abundance is normalized among reported taxa. No reported taxa does not establish absence of organisms.
| Species | Genus | Phylum | Abundance |
|---|---|---|---|
| Campylobacter showae | Campylobacter | Pseudomonadota | 18.65821% |
| Streptococcus salivarius | Streptococcus | Bacillota | 9.98075% |
| Streptococcus anginosus | Streptococcus | Bacillota | 9.48890% |
| Haemophilus parainfluenzae | Haemophilus | Pseudomonadota | 8.60998% |
| Mycoplasma iguanae | Mycoplasma | Mycoplasmatota | 7.44385% |
| Veillonella parvula | Veillonella | Bacillota | 7.02464% |
| Methanococcus vannielii | Methanococcus | Methanobacteriota | 5.43842% |
| Streptococcus sanguinis | Streptococcus | Bacillota | 5.43726% |
| Veillonella rodentium | Veillonella | Bacillota | 3.46824% |
| Haemophilus influenzae | Haemophilus | Pseudomonadota | 3.14212% |
| Campylobacter gracilis | Campylobacter | Pseudomonadota | 1.72861% |
| Streptococcus gordonii | Streptococcus | Bacillota | 1.70817% |
| Streptococcus downei | Streptococcus | Bacillota | 1.52145% |
| Methanococcus maripaludis | Methanococcus | Methanobacteriota | 1.51164% |
| Campylobacter sputorum | Campylobacter | Pseudomonadota | 1.33744% |
| Streptococcus pneumoniae | Streptococcus | Bacillota | 1.32970% |
| Veillonella dispar | Veillonella | Bacillota | 1.32327% |
| Streptococcus mitis | Streptococcus | Bacillota | 1.25615% |
| Campylobacter ureolyticus | Campylobacter | Pseudomonadota | 1.01764% |
| Haemophilus pittmaniae | Haemophilus | Pseudomonadota | 0.98527% |
| Campylobacter concisus | Campylobacter | Pseudomonadota | 0.86228% |
| Granulicatella balaenopterae | Granulicatella | Bacillota | 0.83395% |
| Streptococcus oralis | Streptococcus | Bacillota | 0.82378% |
| Streptococcus periodonticum | Streptococcus | Bacillota | 0.78461% |
| Mycoplasma testudinis | Mycoplasma | Mycoplasmatota | 0.74864% |
| Streptococcus pyogenes | Streptococcus | Bacillota | 0.66161% |
| Haemophilus haemoglobinophilus | Haemophilus | Pseudomonadota | 0.63422% |
| Campylobacter curvus | Campylobacter | Pseudomonadota | 0.62932% |
| Veillonella seminalis | Veillonella | Bacillota | 0.58193% |
| Campylobacter jejuni | Campylobacter | Pseudomonadota | 0.51888% |
| Haemophilus aegyptius | Haemophilus | Pseudomonadota | 0.50906% |
31 of 31 reported species have an eligible reference. MAFFT alignment and FastTree GTR+CAT tree, pruned to this sample. This is not a phylogeny inferred from sample reads or ASVs. Root placement is arbitrary; branch lengths are substitutions per site.
Files contain the original full run. Downloads are hosted by ENA.
| File | Type / bytes | MD5 |
|---|---|---|
| SRR33005188_1.fastq.gz | FASTQ / 145151828 | 548561e42eb14d580c80420d1d599d4e |
| marker | 16S |
|---|---|
| pipeline | Archaions v18.8 |
| read_sampling | First available reads, not random subsampling |
| input_sha256 | faa942786251fc9b6452b4ca5735f3c96ede2997807563075174a3c4bdb2bf41 |
| median_read_length | 554.0 |
| reads_in_length_window | 5257 |
| length_window_bp | [1200, 2000] |
| quality_scores | Unavailable in fetched FASTA; no measured quality filtering |
| classifier_stats | {"marker": "16s", "pipeline": "v18.8", "gpu": "RTX-PRO-6000", "input_path": "volume-fastq-gz", "reads_in": 20000, "reads_skipped": 14547, "elapsed_seconds": 1.5124750770000048, "reads_submitted": 20000, "reads_after_filter": 20000, "adapter_scan": {"sampled": 200, "matched": 55, "fraction": 0.275, "adapters_found": {"27F": 55}, "should_trim": true}, "porechop_ran": false, "porechop_reason": "fast-path: no adapter trimming required"} |
All retrieved values are included. Blank source values are displayed as “Not reported”. Expand the sections below to inspect the full record.
| run_accession | SRR33005188 |
|---|---|
| age | Not reported |
| aligned | Not reported |
| altitude | Not reported |
| assembly_quality | Not reported |
| assembly_software | Not reported |
| bam_aspera | Not reported |
| bam_bytes | Not reported |
| bam_file_role | Not reported |
| bam_ftp | Not reported |
| bam_galaxy | Not reported |
| bam_md5 | Not reported |
| base_count | 152751130 |
| binning_software | Not reported |
| bio_material | Not reported |
| bisulfite_protocol | Not reported |
| broad_scale_environmental_context | Not reported |
| broker_name | Not reported |
| cage_protocol | Not reported |
| cell_line | Not reported |
| cell_type | Not reported |
| center_name | SUB15232776 |
| checklist | Not reported |
| chip_ab_provider | Not reported |
| chip_protocol | Not reported |
| chip_target | Not reported |
| collected_by | Not reported |
| collection_date | Not reported |
| collection_date_end | Not reported |
| collection_date_start | Not reported |
| completeness_score | Not reported |
| contamination_score | Not reported |
| control_experiment | Not reported |
| country | Not reported |
| cultivar | Not reported |
| culture_collection | Not reported |
| datahub | dcc_metagenome |
| depth | Not reported |
| description | MinION sequencing: Full-length 16S sequencing of human supragingival swab from Alzheimer patients and healthy controls |
| dev_stage | Not reported |
| disease | Not reported |
| dnase_protocol | Not reported |
| ecotype | Not reported |
| elevation | Not reported |
| environment_biome | Not reported |
| environment_feature | Not reported |
| environment_material | Not reported |
| environmental_medium | Not reported |
| environmental_sample | Not reported |
| experiment_accession | SRX28271269 |
| experiment_alias | pt25 sup 16S full-length |
| experiment_target | Not reported |
| experiment_title | MinION sequencing: Full-length 16S sequencing of human supragingival swab from Alzheimer patients and healthy controls |
| experimental_factor | Not reported |
| experimental_protocol | Not reported |
| extraction_protocol | Not reported |
| faang_library_selection | Not reported |
| fastq_aspera | fasp.sra.ebi.ac.uk:/vol1/fastq/SRR330/088/SRR33005188/SRR33005188_1.fastq.gz |
| fastq_bytes | 145151828 |
| fastq_file_role | GENERATED_FILE |
| fastq_ftp | ftp.sra.ebi.ac.uk/vol1/fastq/SRR330/088/SRR33005188/SRR33005188_1.fastq.gz |
| fastq_galaxy | ftp.sra.ebi.ac.uk/vol1/fastq/SRR330/088/SRR33005188/SRR33005188_1.fastq.gz |
| fastq_md5 | 548561e42eb14d580c80420d1d599d4e |
| file_location | Not reported |
| first_created | 2025-04-08 |
| first_public | 2025-04-08 |
| germline | Not reported |
| hi_c_protocol | Not reported |
| host | Not reported |
| host_body_site | Not reported |
| host_genotype | Not reported |
| host_gravidity | Not reported |
| host_growth_conditions | Not reported |
| host_phenotype | Not reported |
| host_scientific_name | Not reported |
| host_sex | Not reported |
| host_status | Not reported |
| host_tax_id | Not reported |
| identified_by | Not reported |
| instrument_model | MinION |
| instrument_platform | OXFORD_NANOPORE |
| investigation_type | Not reported |
| isolate | Not reported |
| isolation_source | Not reported |
| last_updated | 2025-04-08 |
| lat | Not reported |
| library_construction_protocol | Not reported |
| library_gen_protocol | Not reported |
| library_layout | SINGLE |
| library_max_fragment_size | Not reported |
| library_min_fragment_size | Not reported |
| library_name | pt25 sup 16S full-length |
| library_pcr_isolation_protocol | Not reported |
| library_prep_date | Not reported |
| library_prep_date_format | Not reported |
| library_prep_latitude | Not reported |
| library_prep_location | Not reported |
| library_prep_longitude | Not reported |
| library_selection | PCR |
| library_source | GENOMIC |
| library_strategy | AMPLICON |
| local_environmental_context | Not reported |
| location | Not reported |
| location_end | Not reported |
| location_start | Not reported |
| lon | Not reported |
| marine_region | Not reported |
| mating_type | Not reported |
| ncbi_reporting_standard | Not reported |
| nominal_length | Not reported |
| nominal_sdev | Not reported |
| pcr_isolation_protocol | Not reported |
| ph | Not reported |
| project_name | Not reported |
| protocol_label | Not reported |
| read_count | 191760 |
| read_strand | Not reported |
| restriction_enzyme | Not reported |
| restriction_enzyme_target_sequence | Not reported |
| restriction_site | Not reported |
| rna_integrity_num | Not reported |
| rna_prep_3_protocol | Not reported |
| rna_prep_5_protocol | Not reported |
| rna_purity_230_ratio | Not reported |
| rna_purity_280_ratio | Not reported |
| rt_prep_protocol | Not reported |
| run_alias | patient25.fastq.gz |
| run_date | Not reported |
| salinity | Not reported |
| sample_accession | SAMN47767906 |
| sample_alias | Not reported |
| sample_capture_status | Not reported |
| sample_collection | Not reported |
| sample_description | Not reported |
| sample_material | Not reported |
| sample_prep_interval | Not reported |
| sample_prep_interval_units | Not reported |
| sample_storage | Not reported |
| sample_storage_processing | Not reported |
| sample_title | Not reported |
| sampling_campaign | Not reported |
| sampling_platform | Not reported |
| sampling_site | Not reported |
| scientific_name | Not reported |
| secondary_project | Not reported |
| secondary_sample_accession | SRS24617399 |
| secondary_study_accession | SRP573912 |
| sequencing_date | Not reported |
| sequencing_date_format | Not reported |
| sequencing_location | Not reported |
| sequencing_longitude | Not reported |
| sequencing_method | Not reported |
| sequencing_primer_catalog | Not reported |
| sequencing_primer_lot | Not reported |
| sequencing_primer_provider | Not reported |
| serotype | Not reported |
| serovar | Not reported |
| sex | Not reported |
| specimen_voucher | Not reported |
| sra_aspera | Not reported |
| sra_bytes | Not reported |
| sra_file_role | Not reported |
| sra_ftp | Not reported |
| sra_galaxy | Not reported |
| sra_md5 | Not reported |
| status | public |
| strain | Not reported |
| study_accession | PRJNA1243403 |
| study_alias | PRJNA1243403 |
| study_title | Oral microbiota of patients with Alzheimer's disease and healthy controls |
| sub_species | Not reported |
| sub_strain | Not reported |
| submission_accession | SRA2107598 |
| submission_tool | Not reported |
| submitted_aspera | Not reported |
| submitted_bytes | Not reported |
| submitted_file_role | Not reported |
| submitted_format | Not reported |
| submitted_ftp | Not reported |
| submitted_galaxy | Not reported |
| submitted_host_sex | Not reported |
| submitted_md5 | Not reported |
| submitted_read_type | Not reported |
| surveillance_target | Not reported |
| tag | Not reported |
| target_gene | Not reported |
| tax_id | Not reported |
| tax_lineage | Not reported |
| taxonomic_classification | Not reported |
| taxonomic_identity_marker | Not reported |
| temperature | Not reported |
| tissue_lib | Not reported |
| tissue_type | Not reported |
| transposase_protocol | Not reported |
| variety | Not reported |
| alias | Patient25 supragingival 16S_full-length |
|---|---|
| title | MIMARKS Survey related sample from human oral metagenome |
| description | Not reported |
| source | NCBI BioSample |
| collection_date | 2023 |
|---|---|
| env_broad_scale | Human supragingival swab patient25 |
| env_local_scale | Department of Psychiatry of the LVR-Klinikum Dsseldorf |
| env_medium | supragingival swab |
| geo_loc_name | Germany: Dsseldorf |
| host | Homo sapiens |
| lat_lon | 51.227700 N 6.77350 E |
| run | SRR33005188 |
|---|---|
| sample | SAMN47767906 |
| study | PRJNA1243403 |
| title | Not reported |
| alias | Patient25 supragingival 16S_full-length |
| site | Plaque |
| subject | Patient25 |
| phenotype | Patient |
| sex | Not reported |
| smoking | Not reported |
| periodontitis | Not reported |
| time_point | Not reported |
| negative_control | False |
| lab_model | False |
| state | complete |
| reads_input | 20000 |
| species_reported | 31 |
| human_primary | True |
Model-based taxonomy; research use. This report does not provide a diagnosis or a validated health score.